make min_read_support in get_candidate_pos a command params

[yangmqglobe]

The min_read_support in get_candidate_pos in phaser.py can't be adjust in command line, 5 is too small for amplicon sequencing, some high quality SNP is missing in "sites_for_phasing".

[xiao-chen-xc]

Hi @yangmqglobe are you using the targeted mode? There is the --min-variant-frequency option.
See https://github.com/PacificBiosciences/paraphase/blob/main/docs/targeted_data.md#command-line-options

[yangmqglobe]

paraphase/paraphase/phaser.py

Line 960 in a72afbc

del_bases_count < min_read_support

min_read_support skip those position which has larger del_bases_count , which is commom in amplicon data becouse of larger coverage. May be this should judge by min_vaf?

[xiao-chen-xc]

To get around that problem, I think you can try downsampling your data. The super high coverage of amplicon data is not really necessary. ~100X per haplotype is good enough.

[yangmqglobe]

Thanks for your sugguestion. I also figure out that I can call variants with existiing caller such as deepvariants and feed them into the process by add_sites config.